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Phthalate acid esters (PAEs) are commonly used plastic additives, not chemically bound to the plastic that migrate into surrounding environments, posing a threat to environmental and human health. Dibutyl phthalate (DBP) and di(2-ethylhexyl) phthalate (DEHP) are two common PAEs found in agricultural soils, where degradation is attributed to microbial decomposition. Yet the impact of the plastic matrix on PAE degradation rates is poorly understood. Using 14C-labelled DBP and DEHP we show that migration from the plastic matrix into soil represents a key rate limiting step in their bioavailability and subsequent degradation. Incorporating PAEs into plastic film decreased their degradation in soil, DBP (DEHP) from 79% to 21% (9% to <1%), over four months when compared to direct application of PAEs. Mimicking surface soil conditions, we demonstrated that exposure to ultraviolet radiation accelerated PAE mineralisation twofold. Turnover of PAE was promoted by the addition of biosolids, while the presence of plants and other organic residues failed to promote degradation. We conclude that PAEs persist in soil for longer than previously thought due to physical trapping within the plastic matrix, suggesting PAEs released from plastics over very long time periods lead to increasing levels of contamination.

Dissolved organic matter (DOM) plays a fundamental role in nutrient cycling dynamics in riverine systems. Recent research has confirmed that the concentration of riverine DOM is not the only factor regulating its functional significance; the need to define the chemical composition of DOM is a priority. Past studies of riverine DOM rested on bulk quantification, however technological advancements have meant there has been a shift towards analytical methods which allow the characterisation of DOM either at compound class or more recently molecular level. However, it is important to consider that all analytical methods only consider a defined analytical window. Thus, herein, we explore the use of a hierarchy of methods which can be used in combination for the investigation of a wide range of DOM chemistries. By using these methods to investigate the DOM composition of a range of streams draining catchments of contrasting environmental character, a wide range of compounds were identified across a range of polarities and molecular weight, thereby extending the analytical window. Through the elucidation of the DOM character in stream samples, information can be collected about likely the sources of DOM. The identification of individual key compounds within the DOM pool is a key step in the design of robust and informative bioassay experiments, used to understand in-stream ecosystem responses. This is critical if we are to assess the role of DOM as a bioavailable nutrient resource and/or ecotoxicological factor in freshwater.

In fresh waters, the origins of dissolved organic matter (DOM) have been found to exert a fundamental control on its reactivity, and ultimately, its ecosystem functional role. A detailed understanding of landscape scale factors that control the export of DOM to aquatic ecosystems is, therefore, pivotal if the effects of DOM flux to fresh waters are to be fully understood. In this study we present data from a national sampling campaign across the United Kingdom in which we explore the variability in DOM composition in three broad landscape types defined by similar precipitation, geology, land use and management, hydrology, and nutrient enrichment status. We characterised samples from fifty-one sites, grouping them into one of three major underlying classifications: circumneutral streams underlain by clay and mudstone (referred to as ‘clay’), alkaline streams underlain by Cretaceous Chalk or by Carboniferous or Jurassic Limestone (‘limestone’), and acidic streams in peatland catchments underlain by a range of low permeability lithologies (‘peat’). DOM composition was assessed through organic matter stoichiometry (organic carbon: organic nitrogen; organic carbon: organic phosphorus; C/N(P)DOM) and metrics derived from ultra-violet (UV)/visible spectroscopic analysis of DOM such as specific UV absorption (a254 nm; SUVA254). We found similar SUVA254, C/NDOM and DOM/a254 relationships within classifications, demonstrating that despite a large degree of heterogeneity within environments, catchments with shared environmental character and anthropogenic disturbance export DOM with a similar composition and character. Improving our understanding of DOM characterisation is important to help predict shifts in stream ecosystem function, and ecological responses to enrichment or mitigation efforts and how these may result in species composition shifts and biodiversity loss in freshwater ecosystems.

The leaching of base cations in acidic soils can result in calcium (Ca2+) and magnesium (Mg2+) deficiencies, which are important for microbial cell function. We aimed to determine if microbial carbon use efficiency (CUE) and microbial biomass carbon (MBC) were limited in acidic soils due to a lack of base cations. Microbial CUE across a range of agricultural soils (n = 970; pHCa 3.4–7.9) treated with either deionised H2O (control) or a solution of 300 mM CaCl2 + 300 mM MgCl2 (+Base cations) was determined using a14C radioisotope tracer approach. Our results showed that the addition of base cations significantly increased microbial CUE (by up to 20%) at pHCa < 4.7; which coincided with a steep increase in exchangeable acidity. Base cation addition significantly increased MBC in nil-limed soils (pHCa 4.6) from 494 mg C kg−1 to 769 mg C kg−1 when plant residue was added, but not in limed soils (pHCa 6.2). Our findings indicate that the addition of base cations to highly acidic soils can increase microbial growth, thus aiding with carbon sequestration in these agricultural soils.

Rapidly assessing biodiversity is essential for environmental monitoring; however, traditional approaches are limited in the scope needed for most ecological systems. Environmental DNA (eDNA) based assessment offers enhanced scope for assessing biodiversity, while also increasing sampling efficiency and reducing processing time, compared to traditional methods. Here we investigated the effects of landuse and seasonality on headwater community richness and functional diversity, via spatio-temporal dynamics, using both eDNA and traditional sampling. We found that eDNA provided greater resolution in assessing biodiversity dynamics in time and space, compared to traditional sampling. Community richness was seasonally linked, peaking in spring and summer, with temporal turnover having a greater effect on community composition compared to localized nestedness. Overall, our assessment of ecosystem function shows that community formation is driven by regional resource availability, implying regional management requirements should be considered. Our findings show that eDNA based ecological assessment is a powerful, rapid and effective assessment strategy that enables complex spatio-temporal studies of community diversity and ecosystem function, previously infeasible using traditional methods.

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Dissolved organic matter (DOM) is a complex mixture of carbon-containing compounds. The low-molecular weight (LMW) fraction constitutes thousands of different compounds and represents a substantial proportion of DOM in aquatic ecosystems. The turnover rates of this LMW DOM can be extremely high. Due to the challenges of measuring this pool at a molecular scale, comparatively little is known of the fate of LMW DOM compounds in lotic systems. This study addresses this knowledge gap, investigating the microbial processing of LMW DOM across 45 sites representing a range of physicochemical gradients and dominant land covers in the United Kingdom. Radioisotope tracers representing LMW dissolved organic carbon (DOC) (glucose), dissolved organic nitrogen (DON) (amino acid mixture), dissolved organic phosphorus (DOP) (glucose-6-phosphate), and soluble reactive phosphorus (SRP, measured as orthophosphate) were used to measure the microbial uptake of different DOM compounds in river waters. The amount of DOM biodegradation varied between different components (DON ≥ DOC > DOP), with the rate of turnover of all three increasing along a gradient of N and P enrichment across the range of sites. Conversely, the uptake of SRP decreased along this same gradient. This was ascribed to preferential utilization of DOP over SRP. Dominant land cover had a significant effect on DOM use as a resource, due to its control of nutrient enrichment within the catchments. We conclude that nutrient enrichment of river waters will lead to further DOM removal from the water column, increased microbial growth, and a decrease in stream oxygen saturation, exacerbating the effects of eutrophication in rivers.

Sulphur (S) is a key macronutrient for all organisms, with similar cellular requirements to that of phosphorus (P). Studies of S cycling have often focused on the inorganic fraction, however, there is strong evidence to suggest that freshwater microorganisms may also access dissolved organic S (DOS) compounds (e.g. S-containing amino acids). The aim of this study was to compare the relative concentration and depletion rates of organic 35S-labelled amino acids (cysteine, methionine) with inorganic S (Na235SO4) in oligotrophic versus mesotrophic river waters draining from low nutrient input and moderate nutrient input land uses respectively. Our results showed that inorganic SO42− was present in the water column at much higher concentrations than free amino acids. In contrast to SO42−, however, cysteine and methionine were both rapidly depleted from the mesotrophic and oligotrophic waters with a halving time < 1 h. Only a small proportion of the DOS removed from solution was mineralized and excreted as SO42− (< 16% of the total taken up) suggesting that the DOS could be satisfying a demand for carbon (C) and S. In conclusion, even though inorganic S was abundant in freshwater, it appears that the aquatic communities retained the capacity to take up and assimilate DOS.

Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0–20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by “E-plasma,” “A-plasma,” other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.

Dissolved organic matter (DOM) plays an important role in freshwater biogeochemistry. To investigate the influence of catchment character on the quality and quantity of DOM in freshwaters, 45 sampling sites draining subcatchments of contrasting soil type, hydrology, and land cover within one large upland-dominated and one large lowland-dominated catchment were sampled over a 1-yr period. Dominant land cover in each subcatchment included: arable and horticultural, blanket peatland, coniferous woodland, and improved, unimproved, acid, and calcareous grasslands. The composition of the C, N, and P pool was determined as a function of the inorganic nutrient species (NO3−, NO2−, NH4+, and PO43−) and dissolved organic nutrient (dissolved organic carbon [DOC], dissolved organic nitrogen [DON], and dissolved organic phosphorus [DOP]) concentrations. DOM quality was assessed by calculation of the molar DOC : DON and DOC : DOP ratios and specific ultraviolet absorbance (SUVA254). In catchments with little anthropogenic nutrient inputs, DON and DOP typically composed > 80% of the total dissolved nitrogen (TDN) and total dissolved phosphorus (TDP) concentrations. By contrast, in heavily impacted agricultural catchments DON and DOP typically comprised 5–15% of TDN and 10–25% of TDP concentrations. Significant differences in DOC : DON and DOC : DOP ratios were observed between land cover class with significant correlations observed between both the DOC : DON and DOC : DOP molar ratios and SUVA254 (rs = 0.88 and 0.84, respectively). Analysis also demonstrated a significant correlation between soil C : N ratio and instream DOC : DON/DOP (rs = 0.79 and 0.71, respectively). We infer from this that soil properties, specifically the C : N ratio of the soil organic matter pool, has a significant influence on the composition of DOM in streams draining through these landscapes.

Dissolved organic matter (DOM) represents a key component of carbon (C) cycling in freshwater ecosystems. While the behaviour of bulk dissolved organic carbon (DOC) in aquatic ecosystems is well studied, comparatively little is known about the turnover of specific DOC compounds. The aim of this study was to investigate the persistence of 14C-labelled low molecular weight (LMW) DOC at a wide range of concentrations (0.1 µM to 10 mM), in sediments and waters from oligotrophic and mesotrophic rivers within the same catchment. Overall, rates of DOC loss varied between compound groups (amino acids > sugars = organic acids > phenolics). Sediment-based microbial communities contributed to higher DOC loss from river waters, which was attributed, in part, to its greater microbial biomass. At higher DOC compound concentrations, DOC loss was greater in mesotrophic rivers in comparison to oligotrophic headwaters. A lag-phase in substrate use within sediments provided evidence of microbial growth and adaptation, ascribed here to the lack of inorganic nutrient limitation on microbial C processing in mesotrophic communities. We conclude that the higher microbial biomass and available inorganic nutrients in sediments enables the rapid processing of LMW DOC, particularly during high C enrichment events and in N and P-rich mesotrophic environments.

Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host–microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.